User:Wayne Decatur/Generate Unfolded Structures

This describes how to unfold whole or parts of chains in solved structures using Pymol. This maintains the covalent bonds. Also below is how to alter disulfide bonds in a structure using Pymol.

This came up because Adriana Zeledon wanted to generate structures derived from her structure of interest where parts were unfolded or folded differently. I thought this could very useful for illustrative or conceptualizing purposes for many users. For maybe simulating denaturing, conformational changes, or other dynamic processes.

Please note that while maintaining covalent bonds, this process will generate a distorted structure that is just for representational purposes and is not thermodynamically stable. To translate or rotate a chain or parts relative the rest of the structure see my page on moving parts or components of structures using Pymol.

To enable yourself to 'drag' a chain in a structure however you want:

 * Load the structure into Pymol with all the consoles open.
 * Toggle in the bottom right corner the text next to 'Selecting' until 'Residues' comes up. ('Selecting' currently shows as 'Picking' in Mac Pymol1.3r1.)
 * put the mouse into 3-button editing mode either using 'Mouse' menu in upper console or toggle it by clicking text next to 'Mouse mode'. (On Max currently doing this causes the 'Picking' setting to look like it changes to atoms but holding down control key on the Mac and dragging with left click still drags chain around elastic and over time it settles to a form where bonds still constrained to proper length. )
 * Click on Auto-Sculpting in the Sculpting menu that is under the Build menu.
 * Use control-left-click-and-drag to click on the chain of interest and drag to move the chain where you want it to go and it will move towards your mouse like it is trying to catch up but is in viscous solution.
 * When things are where you want for that part of the chain, quickly click 'Deactivate' under the Sculpting menu. The chain will freeze where it is.
 * If you view in cartoons you will see that the secondary structure assignments are maintained from before you modified the structure. To recalculate the secondary structure based on the new one enter in the command line 'dss [object-name/pdb-code]'
 * Save your modified structure.

Disulfide bonds are covalent bonds that will remain maintained when you do the above process; however this may not be the behavior you wish for some or all of these bonds. You may wish to break the disulfides to unfold the protein more than you could obtain if you did not using the above process.

Breaking disulfide bonds with Pymol:

 * Either pick the two atoms (pk1 and pk1, they will be called in the list to the side in Pymol) in the bond by going into 3 button Editing mode and selecting the bond between the two atoms and hitting Ctrl-right-click or choose atom #1 (pk1) first by hitting Ctrl-middle-click as you touch the atom and then selecting the next (pk2) and doing the same. You will see '(pk1)' and '(pk2)' in the list to the right of the structure.
 * Once the two atoms are chosen, break the bond by entering 'unbond pk1,pk2' in a command line area in Pymol.
 * 1gxv is a good structure to with which to try this.

If you want to form new disulfide bonds after you modified the structure:

 * Use the 'bond' command to link the gamma sulfur atoms of the resides of interest. For example, if we were joining residues 37 and 82, 'bond 37/sg,82/sg'
 * Then enter the command 'unpick' to hide the 'bond baton' that gets displayed.

Morphing
To make clear the changes that took place to get to the modified structure, you may want to submit the original and modified structures to the Yale Morph Server and let it generate the steps needed to go from one structure to the other and make an animation with this collection of structures. You may wish to look at the Morphs page or Eric Martz's page on the lac repressor morphs or  my page on a complex morph that I did for more information on creating morphs.

Pages with supporting information
Bold text
 * Modeling and Editing Structures Page at Pymol Wiki
 * Posting about using Sculpting in Pymol to manipulate structures
 * Has information on molecular sculpting with a summary of what it is meant to be
 * Pymol tips list with some help about moving molecules and parts of structures around
 * Pymol Users manual page on secondary structure